The first problem is best rephrased as "I have an existing ontology and I wish to express statements using the terminology defined in that ontology". The simple answer is "create individuals in protege that conform to the constraints expressed by your terminology".
These things probably sound foreign. The real problem is that your question suggests that you have little knowledge of RDF/OWL and you're attempting to dive way too deep way too fast. For example: if I were to ask a question that involved complex XSLT transformations when I didn't even know how to write XML, I'd be down-voted into oblivion and barraged with comments stating: "RTFM".
The question "how do I use this ontology" is answered thusly:
Read the RDF 1.1 Primer and the Jena Tutorials
Read the OWL 2 Primer and read the Jena Ontology API documentation.
Then you will be ready to:
- Read the submitted specification for OWL-S
Apache Jena does not support SWRL rules out-of-the-box, so you will need to identify a Jena-compatable reasoner that does (such as Pellet), or learn how to utilize Apache Jena's Rule Engines. Your particular problem may not require rules to solve at all (for example, you may be able to identify service equivalence using owl2-keys). Either way, once you have decided what rule domain you are working in, you will be ready to face the problem of:
- Write equivalency rules or add equivalency axioms for OWL-S service descriptions.